After the Storm
by Hatcheter
Summary: The storm has passed, and John Sheppard must pick up the pieces.
1. Okay

Disclaimer: I don't own anything except the computer I wrote this little piece on. If the rightful owners of the characters and stories are offended, I'll gladly take it down.

Spoilers: The Eye (Atlantis112)

**After the Storm**  
by Hatcheter

**I – Okay**

"Dr. Weir?"

Elizabeth started as Major Sheppard's voice broke the calm of the empty control center.

"Has the storm passed?" he asked, joining her where she stood just inside the open balcony door. The rain fell lightly, driven by a gentle wind. Distant lighting flashed sporadically on the horizon.

Elizabeth shrugged. "It started to die down about fifteen minutes ago."

Sheppard examined her out of the corner of his eye as she continued to stare straight ahead. She was slouched against the doorframe, her arms crossed tightly across her chest. Her eyes were distant, tired. She wasn't watching the storm recede.

"How long have you been standing here?" he asked.

"About an hour," she dully answered.

Sheppard frowned at her. "You're getting wet, Doctor Weir. Come on." Gently taking her arm, he tugged her away from the door.

Elizabeth looked down, noticing for the first time that her pants were soaked from the knees down. Her shoes squished as she walked, squeezing water out of her socks with each step.

"Where is everyone else?" she asked.

"Ford and McKay took Doctor Beckett up to the jumper bay," the Major explained. "The doctor's got a nasty bump on his head, and the Jumpers have the only medical supplies we can get to until the lightning stops. Teyla's there as well, so she and those Athosian kids can guard her prisoner."

"We'll have to do something with her," Weir said.

"We've got holding cells. And," he added dryly, "We won't have problems feeding this prisoner."

Sheppard guided Elizabeth down the main stairs, still holding onto her arm. Ignoring the dead Genii in front of the Stargate, he turned the woman toward a side corridor. There were several small, decently furnished rooms off of the main corridor, which they had assumed were receiving rooms for travelers. Some were now used for storage; others were for the gate room guards.

He took her into one of the latter, guiding her to a long couch. After she sat down, he turned to the trunk in the corner of the room.

"You shot him."

Sheppard pulled a pillow and blanket out of the trunk and turned back to Elizabeth. "He would have taken you through the gate."

"So you killed him."

He knelt on the floor in front of Elizabeth. Reaching out, he lifted up one of her feet and set it on his lap. "I killed a lot of people today," he said softly as he began to untie her shoelace.

Elizabeth snorted bitterly. "So, what, you want a medal?"

John's fingers briefly faltered. Shaking his head, he pulled off her shoe, then her sock. "No." Setting her bare foot on the floor, he picked up the other one and started the process over.

"No medals, no commendations, no praise filled after action reports." Rising, he turned and set the shoes and socks on the trunk, spreading them out so they could dry. "Everyone's still here."

"You could have hit me," she whispered.

Sighing, he turned back, looking firmly into her tired eyes. "I wouldn't have fired if there was a chance of that."

"How could you be certain that…"

John sat down heavily, bouncing Elizabeth and effectively silencing her. "You're not very familiar with guns, are you?"

She shook her head. "I hate the things."

"Well, I think you need to learn how to use one. Just in case you need to defend yourself."

She frowned. "I don't know about that."

"If McKay can learn, anybody can."

"Rodney's a genius," she said.

John smiled. "Yes, he keeps reminding me about that. But then again, when it comes to stripping and cleaning his weapons he's all thumbs."

Elizabeth smiled as well, slouching back on the couch. She suddenly sat upright, looking around alertly. "If the storm has passed, Rodney can disable the shield generators. We should recall our people and-"

John put a hand on her shoulder, pulling her back down on the couch as she tried to stand. "Relax," he said, gently pushing her toward her pillow. "It's still the middle of the night on Manera, too. We've got six hours until dawn; we can call them home then."

"What about-" she began.

"I'll look after things," he assured her.

Willing the lights off, he stood and unfolded the blanket. "You'll be okay, Elizabeth," John promised, smiling gently as he tucked her in.

She pulled the blanket close to her body, shivering when she realized just how cold she was.

And she smiled back, because she believed him.

* * *

Author's notes: I was inspired to write this after seeing "The Eye". It feels like a good way to stick a toe into SG fan fiction.

I love the mix of shock and honesty Weir's voice when she says "no", and Sheppard's confident "you will be". While all the Shep/Weir shippers see a lot in that, I think it's a good moment of honesty between two leaders who have come to trust and rely on each other.

I'm personally not sold on the Shep/Weir idea, or any other ship in Atlantis. That idea has growing on me, though.

Though it's not my intent with this piece, I won't be offended if people see this as 'pre-ship'. :)

So please, drop me a review at , or wherever you happen to read this.  



	2. One Night

**II – One Night**

Sheppard let the door slide closed. He walked a few paces and stopped. Elizabeth was exhausted, and he wanted to be sure that she didn't try to slip back to her office after he left. He strained his ears, listening for any sound of restlessness. Or worse, that she might be too shaken or frightened to sleep.

He waited five minutes before the sound of gentle snoring came from the darkened room. Smiling to himself, he turned for the 'Gate room. He walked slowly, wary of making any sound.

The halls were dim, and the air was as quiet and cool as the moment he first stepped out of the Stargate. The city's incredible age was almost palpable. Atlantis had weathered many storms like the ones it had seen tonight, inside and out, and it would do so again.

Reaching the 'Gate room, he was snapped back to the present. Dead Genii littered the room where he and Ford had cut them down as they fled. Sheppard stepped forward and swiftly kicked one of the bodies, watching in morbid fascination as it rolled over. The man, the intruder, stared up at him. Sheppard shuffled back, raising his weapon, before he realized the man was dead. Those eyes were frozen in surprise, accusing him of snatching the life away.

Sheppard turned and hurried up the stairs to the control center, suddenly unsure of himself. If there were survivors, would he offer them aid, or a final bullet? He wasn't sure which course of action would be right, or which was just.

Sheppard toggled his radio. "McKay, are you there?"

_"Yeah?"_ Even over the radio, McKay was curt.

"Can we reconnect the grounds so we can get out into the city again?"

_"Sure,"_ McKay replied. "It'll be pretty simple to do."

"Now?" Sheppard added.

_"Go right ahead."_

Sheppard growled. "I don't know what to do with the computers," he said.

_"I'm indisposed at the moment. Unless you know how to bandage a deep laceration, or at least care for a concussion, that is."_

"Fine," Sheppard barked. "Get yourself patched up."

Sheppard crossed the control room to the dialing computer. Punching in the address for the Maneran's world, he walked onto the balcony as the wormhole exploded into existence, turning his radio on again.

"This is Major Sheppard calling the Atlantis expedition team, please respond." It was less than a minute before he got a reply.

_"Major, this is Sergeant Bates."_

"What's your situation, Sergeant?"

_"Everything is good here, sir,"_ Bates replied. _"The Manerans have generally ignored us. I've got a few men standing watch, but everyone else is sleeping."_

"Any sign of the Genii?"

_"Genii?"_ he asked, puzzled. _"No sir."_

Sheppard sagged against the rail, relieved. "Good. That's good to hear, Sergeant."

_"Sir, has something happened?"_

"The situation has been resolved. I need a few people to come back early and clean things up."

Bates took a few seconds to process the Major's cryptic instructions. _"Understood, sir. I'll get a squad ready and bring them back."_

"Bring someone from the medical staff. And Zelenca, too. Wake them up if you have to."

_"Roger sir. We'll be there in twenty minutes."_

"I'll be waiting."

* * *

Author's note: I had originally intended this story to just be a one-shot, but I just couldn't leave it alone. 


	3. Owe You One

**After the Storm**

**III – Owe You One**

Minister Smeden straightened his shirt and rubbed his eyes. Even before dawn, he had to look official. Taking a deep breath, he entered the meeting room. "Major Sheppard, what brings you here at this early hour?"

Sheppard sat at the head of the conference table, chair pushed back and his feet propped up on the polished wood. His pose and expression were the perfect image of relaxation. Particularly, Smeden noted, the relaxed way his hands gripped his weapon.

"I'm sorry to drag you out of bed so early," Sheppard said, waving a hand toward the dark windows. "A funny thing happened last night. I wanted to tell somebody about it. I realized that the only people who would understand the story were on this planet. I've already talked to my own people, so I thought I should share with you, as well."

"Major, I don't understand why anything would be so urgent that you-"

"You don't understand that there's an Athosian in my people's camp with three broken fingers?" Sheppard interrupted, his voice dangerously calm. Smeden edged back toward the door, wondering why he left the armed guards outside the room as Sheppard rose.

"You don't understand that we nearly lost Atlantis thanks to a strike team who knew the city was empty?" Sheppard's eyes darkened as he took a step toward the minister. "You don't understand that two of my men were killed, and the Genii sent more than sixty of their people to their deaths?"

Smeden's eyes widened as he backed away. "I don't…I didn't..."

"You really ought to know better than to let a source you tortured go free. He's bound to talk."

The minister found himself literally backed into a corner. There was nothing left for him to do but confess. "Major Sheppard, I was assured that no one would be hurt. The Genii told us that you had stolen something from them, that they needed to retrieve."

"They didn't mention how they betrayed us?" Sheppard asked. He was in Smeden's face now. "Used us to get intel on the Wraith, then tried to steal our ships and weapons?"

Smeden shook his head quickly, looking down. "I am sorry for the loss of your men, Major Sheppard. If I had known that the Genii had other motives, I would not have contacted them. Our people have been allies for many generations, and I had trusted them."

Sheppard glared down at the man. "Well, there are a lot of dangerous people out there. You need to be careful about who you trust."

"What happens now? Smeden asked.

Sheppard smiled coldly as he backed away from the minister. "I've sent a few of my people back to Atlantis. They'll be bringing the bodies of the dead strike team. After our people gone, you can give you condolences to the Genii."

"Sixty bodies…" Smeden breathed.

Sheppard shook his head. "There aren't any remains for most of them."

The Minister's eyes widened at that statement. What kind of people were these Atlanteans?"

"And after that?" Smeden asked.

"There's still that trade agreement," Sheppard said, smiling coldly. "We'll be in touch."

Smeden sank into a chair after Sheppard left. There was still over an hour until dawn. Not that he would be sleeping.


	4. Extremely Optimistic

**After the Storm**

IV – Extremely Optimistic

Elizabeth shot upright, heart pounding and eyes darting around the unfamiliar surroundings. Kolya, one arm wrapped painfully around her waist, was dragging her toward the Stargate. And then there was the shot.

There was a gentle knock on the door. "Doctor Weir?"

Major Sheppard. He had shot Kolya. He had saved her. And, she now remembered, he had helped her get through the night.

"Come in, Major," she said, pulling the blanket tighter to her body. It was warm, and the room was very cool.

The door slid open and Sheppard entered the room, squinting in the early morning sunlight that streamed in through the window. "Did I wake you?"

Elizabeth shrugged. "It's all right."

"Bad dream?"

She shrugged again. "What time is it?"

"Almost time for people to start returning." He offered her the bundle he carried. "I had Teyla get these for you."

Elizabeth rose, tiptoeing across the cold floor, and took the bundle of clean, dry clothes. "Thank you."

Sheppard shrugged. "Sure."

She examined him closely for a moment. His shoulders were slumped, there were bags under his eyes, and his hair was more disheveled than normal. "Have you slept, Major?"

"Not yet. But if you don't mind, I'm taking the rest of the day off once we get everybody back."

Elizabeth smiled. "Of course."

John smiled back. "Well, I'll go dial Manera and let the team know we're ready for them to come home."

Ten minutes later, Elizabeth entered the 'Gate room to find Zelenka and Bates mopping the floor.

"What's going on?" she asked, being careful not to step on the newly cleaned floor.

"Major Sheppard thought it best if there weren't blood stains everywhere when the civilians returned," Bates said.

"They must all know by now what has happened," Zelenka complained. "Why does it matter? This is killing my back." Elizabeth got the impression that the Marine was doing most of the actual work.

"Where is the Major?" Weir asked.

"Up there," Zelenka grunted, jerking his head toward the control center before he returned to mopping.

Elizabeth climbed the stairs to find John sitting at the dialing computer, his feet propped up on the console's edge. "You can go to bed, if you want to," she said.

"Not until everyone's back. Just in case."

Elizabeth nodded, folding her arms. "Why is it so cold in here?"

"Because _somebody_," he began, throwing a theatrical glare at her, "left the balcony door open all night."

"Oh," she said, with a small, embarrassed smile.

"It's okay," Sheppard replied. "Life support was offline, so we needed the fresh air."

Elizabeth nodded at that logic, watching the men below continue cleaning. While Bates was working his hardest to make the floor shine, Zelenka was preoccupied with examining the blisters that might have been forming on his palms.

"Thanks for last night," Elizabeth said.

John opened his mouth to respond, but was cut off by a loud clatter followed by a string of profanity.

"Rodney?" Elizabeth asked, turning to find the scientists picking his steel mug up off the floor. A dark stain ran down his left leg.

"I'm sorry, I thought I heard you say…" he trailed off, staring wide-eyed at the two of them. Shaking his head, he returned his attention to his empty mug. "That was the last cup too. I'm gonna have to go brew another pot."

Sheppard couldn't help smiling at the murderous glares the scientist threw at the mug. "Why don't you go get yourself some breakfast while you're at it."

"I've still got to-"

"Zelenka can handle it," Sheppard interrupted.

McKay considered that briefly. "Well, okay."

Elizabeth smiled as McKay hurried away. Sheppard looked up at her, amused. "He gets cranky when he hasn't eaten in a while. Well," he added, "crankier than normal."

Her smile turned into a full-blown grin. Things were going to be just fine.


	5. Good for Everybody

After the Storm

V – Good for Everybody

A knock on the window caused Elizabeth to look up. Sheppard leaned in through the open door, a mug in his hand.

"You busy?" he asked.

"Not at the moment," she said, beckoning him in and to a chair. "Did you comb your hair?"

"Huh?" Sheppard ran his hand through his hair, quickly restoring its usual messiness. "I just woke up. It gets all flat when I sleep."

"So that look's intentional?"

John shrugged. "Intentional laziness."

Elizabeth rolled her eyes, leaning back in her chair. "What can I do for you, Major?"

"McKay's running around the city looking for damage, and he asked me to take a Jumper up and look around. I thought you might like to come along."

"Oh?"

"Yeah."

"I still have work to do."

"I'm sure it will be here when we get back."

"That's the problem," Weir said. "We're still trying to figure out what the Genii got away with, searching for damage, and putting the Athosians into temporary quarters until we can get them back to the mainland."

"They know where everything is," Sheppard said. "Have you been out of the city, or even out of this tower, since we got here?"

"I took care of one of the grounding stations yesterday," she pointed out.

"Other than that?"

She sighed. "My work keeps me here."

"Come on," Sheppard cajoled her. "It will only be an hour or so."

"One hour?" Weir asked.

"Sure."

Elizabeth nodded. "I guess I could use a break."

"Great," Sheppard said, jumping to his feet.

"Give me five minutes," she said.

He nodded. "I'll go warm up the Jumper."

She only took four minutes. After making sure that Grodin could keep an eye on things, and would radio her immediately if there was a problem, she took the stairs up to the jumper bay.

No sooner was she onboard than Sheppard closed the aft hatch. The Jumper was already rising to the roof when she sat down beside him.

"Planning on a picnic?" she asked, noticing the basket behind his seat.

"I haven't eat in almost a day," Sheppard said, banking down toward one of the piers. "I woke up because my stomach was starting to implode."

"I'm sure you'll be fine," she said.

"I had a couple Snickers bars already."

"Snickers?" Weir asked. "Where did you get Snickers?"

"One of Beckett's nurses smuggled a case of them with him."

"How did you get them?"

"The Genii stole them."

"Major!"

"I'm kidding," he said, grinning. "I traded her some of these apple things." John reached back into the basket, one hand blindly digging around while he focused on piloting. "Here," he said, pulling a mottled brown object out. "Ignore how it looks."

Elizabeth gently took the fruit. It was slightly soft, and had a sweet scent. Carefully, she took a small bite. "Wow."

"Good, huh?"

"Mm-hm," Elizabeth mumbled, trying to wipe the juice that had leaked from the fruit onto her chin.

"Here, I've got napkins back here somewhere."

"You just concentrate on flying," she said. Turning her seat, she lifted the basket into her lap. "Do you want one of these?"

"I'll get the controls all sticky if I eat one."

There were several more of the apple things in the basket, along with a large, warm thermos (she assumed it was coffee), some of the jerky that the Athosians made from whatever it was they were hunting on the mainland, a few energy bars, another Snickers, and…

"A turkey sandwich?"

Sheppard smiled. "You know how I feel about turkey. Speaking of which, Thanksgiving is coming up soon."

"In another two months."

"I mean Canadian Thanksgiving."

Weir's narrowed her eyes, perplexed. "You're not Canadian."

"McKay is."

"So you think we should celebrate holidays of all the nations on the team?"

John grinned at her. "Only if they involve eating turkey."

Elizabeth rolled her eyes, shook her head, and laughed, all in one motion. "You realize we're having a shortage on turkeys, right?"

"I'm sure there's something that will taste just as good somewhere in this galaxy. I just have to find it."

John continued to grin as Elizabeth laughed again. It was a sound he enjoyed hearing.

He turned on the Jumper's transmitter. "McKay, do you read me?"

_ "I hear you, Major."  
_  
"I've flown over the city. Nothing seems to have floated away."

_ "Did you see any damage?"_

"Some broken windows out on the piers. Other than that, it looks good up here."

"What have you found, Rodney?" Elizabeth asked.

_ "A lot of water," _ McKay replied. _ "The city is pumping it out, though. It ought to be dry by the end of the week."_

"That's good to hear. We'll see you in a little while."

She turned off the radio as Sheppard flew another lazy arc over the city. "Have you ever seen a sunset from space?" he suddenly asked.

Elizabeth shook her head.

"Me neither, actually. I hear it's something to see."

"You haven't?"

"It's not like I had a chance back home," he said. "And here, I tend to be running toward or away from the Wraith."

She nodded.

"So, you wanna?"

"Do we have time?"

"Sure. It's not like we'll have to wait for sunset to come to us."

"Okay."

John grinned and pulled back on the controls, pushing the speed. The Jumper soared up over the planet, breaking free of the atmosphere in seconds. He settled the ship into a low orbit and shut the engines off, then flipped the Jumper around so they could watch the sun sink toward the horizon.

"We still have to name this planet," Weir said.

"Lieutenant Ford wants to call it 'Atlantica'," John replied.

Elizabeth made a face. "That just doesn't sound right."

John nodded. "The Ancients lived here. They must have had a cool name for it."

"I might be able to search their databases for it."

"Why not one of the scientists?"

Elizabeth shrugged. "It seems to minor to pull someone off a project just to learn this planet's proper name."

"So give the job to someone who's ego needs knocked down a few steps. How about Cavanaugh?"

Elizabeth sighed. "He's very misunderstood. One incident were he got upset about a public dressing down when he was only concerned-"

"Hush."

Elizabeth blinked. "What?"

"The sun is setting," John said, pointing forward. The planet below, which had filled their view a few minutes ago, was only a thin crescent, and the sun was rapidly approaching the planet's edge.

Elizabeth held her breath as the sun reached the horizon. The planet's atmosphere turned to a long thin rainbow of color, pale blues, over red and yellow. The sun, glowing orange through the atmosphere, quickly slipped out of sight. A curve of re light hung over the planet a moment more, before it went completely dark.

"Wow," Elizabeth breathed.

"Yeah," John whispered back, turning to her. "So, wanna see the sunrise?"

Elizabeth grinned at him. "Yes."

Still smiling at her, he flipped the Puddle Jumper around to face the coming sunrise.

* * *

Here's a few good pics I found of sunsets from space. 

Sunset pics: 


End file.
